Thank you for this important contribution to neuroimaging tools for analysis of older populations.  Am looking to confirm rsfMRI results previously obtained on an ADNI dataset with AFNI using MNI152 atlas.  Does anyone have experience applying MCALT in AFNI?  I may need just a bit of hand-holding here, but is it correct that in order to use ./MCALT_T1.nii it needs to be skullstripped first? - KAG

Or...to answer my own question, is the template obtained by applying the brain mask (./MCALT_brainmask.nii) to ./MCALT_T1.nii?

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Originally posted by Kamil Grajski:
I don't have a lot of experience with AFNI, but for the direct question of how to get a skull-stripped version, then I agree with your suggestion. You can either use MCALT_brainmask to to exclude voxels that are mostly CSF, or MCALT_TIV to include the original signal for voxels that are mostly CSF and within the TIV. 

Best,
Chris

Got it!  Many thanks for speedy reply.